Hi Maia,

I think all you need to do is make sure phenix_env (or phenix_env.sh) is sourced after the ccp4 setup.

Apparently you invoked the "phenix.pdbtools" command that comes with CCP4, and apparently the CCP4 installation isn't internally consistent. CCP4 bundles the cctbx libraries (which includes mmtbx) mainly because some parts of it are required for the compilation of phaser. I'm not surprised that the Python-based commands don't work; to my knowledge they aren't actually used in CCP4.

Ralf

From: Maia Cherney <[email protected]>
To: [email protected]
Sent: Thursday, April 21, 2011 3:23 PM
Subject: Re: [phenixbb] b factors reporting


To: PHENIX user mailing list<[email protected]>
Date: Thu, 21 Apr 2011 15:09:19 -0600
Subject: Re: [phenixbb] B factor for DNA and Protein
Pavel Afonine wrote:
>
>  Yes, this trivial combination of two commands will do it:
>
>  phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb
>  phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb
>  phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb
>
Dear Pavel,

These commands did not work for me (version 1.7-650). I need to report
average b factors separately for the protein, water, several ligands
and ions, all of them in one chain A.

Traceback (most recent call last):
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py",
line 3, in<module>
  from mmtbx import pdbtools
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/__init__.py",
line 3, in<module>
  import cctbx.array_family.flex
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx/cctbx/array_family/flex.py",
line 1, in<module>
  import scitbx.array_family.flex
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx/scitbx/array_family/flex.py",
line 2, in<module>
  import boost.optional
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/optional.py",
line 1, in<module>
  import boost.python
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py",
line 45, in<module>
  ext = import_ext("boost_python_meta_ext")
File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py",
line 24, in import_ext
  + ["  "+p for p in sys.path]))
ImportError: __import__("boost_python_meta_ext"):
/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib/libboost_python.so:
undefined symbol: PyUnicodeUCS2_AsWideChar
sys.path:
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/iotbx
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/PyCifRW
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/source/phaser
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/libtbx
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib
  /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/share/python
  /usr/lib/python2.6
  /usr/lib/python2.6/plat-linux2
  /usr/lib/python2.6/lib-tk
  /usr/lib/python2.6/lib-old
  /usr/lib/python2.6/lib-dynload
  /usr/lib/python2.6/dist-packages
  /usr/lib/python2.6/dist-packages/Numeric
  /usr/lib/python2.6/dist-packages/PIL
  /usr/lib/python2.6/dist-packages/gst-0.10
  /var/lib/python-support/python2.6
  /usr/lib/python2.6/dist-packages/gtk-2.0
  /var/lib/python-support/python2.6/gtk-2.0
  /usr/local/lib/python2.6/dist-packages


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